Smash/Super Missiles(SM's): SM's are in no way useless. After playing for a while, you should have the timing down for double missiles canceling these, which is really good for shield pressure and keep away tactics. If you are using them for keep away, its also good to throw a zair or two into the mix to add variation. In short, SM's are great as a means of defense. If your opponent shields, they lose a lot of momentum and a lot of shield. If they get hit, they lose a lot of momentum still, they eat 10%, and they get knocked back.
Homing Missiles(HM's): HM's are your go-to technique for approaches and mix-ups (along with zair of course). In Brawl, HM's last longer before exploding, and track your opponent more accurately and have tighter turning. In ground approaches, you can short hop HM cancel to fire them quickley while approaching and set up for combos and add extra damage. The stun is pretty good on these as well. Two excellent maneuvers with HM's are:
1) HM > Zair- You can do this in your approach to kill you opponents momentum, set up for combos, and kill their defense.
2) HM > Charge shot- REALLY REALLY REALLY GOOD FINISHER. I can't stress this enough. Although her charge shots power got nerfed a bit, it is still one of her best KO'ers. HM's set up for a charge shot perfectly. If it hits, and you are at mid range, you can basically gaurantee yourself a charge shot hit. Also HM > down tilt works well for a KO. works the same way as HM > Charge shot, just close range obviously.
Lastly, HM's are great for edge guarding. Knock your opponent off some ways and follow up with full-jump double HM's to make them drop and get gimped, or just give them something else to worry about. In the same way, you can use them to anti-edge guard. Since they come out so fast you can fire off about three on your way back to the stage to help keep your opponent for chasing. Against Marth, only shoot two though.
In a nutshell, SM's are great defensive tools, and HM's are geat offensive tools. I use them interchangeably to keep my opponent from adapting, but this is a basic rundown.